Not to be alarming, but some minor clearancing may be necessary to allow for a pre-drilled neck to lay flat in the pocket without binding on the sides or at the heel. Everyone publishes that 2.5" Fender heel dimension, but sometimes a few .001" can make a difference. It's part of the fun.
I've used Fender MIM, Mighty Mite, and Warmoth necks for various builds and was never satisfied until I applied some localized sanding to the sides of the neck (and resealed with Tru-Oil). In the worst case, the replacement maple neck was thicker top-to-bottom than the MIM rosewood by a substantial amount and required a belt sander modification to allow for reasonable bridge saddle height.